| Options | Valuetype | Default | Descriptions |
| -r | Integer | 1 | Reward for a nucleotide match |
| -f | Integer | 0 | Threshold for extending hits, default if zero |
| -Q | Integer | 1 | Query Genetic code to use |
| -D | Integer | 1 | DB Genetic code (for tblast[nx] only) |
| -J | T/F | F | Believe the query defline |
| -W | Integer | 0 | Word size, default if zero |
| -z | Integer | 0 | Effective length of the database (use zero for the real size) |
| -K | Integer | 100 | Number of best hits from a region to keep |
| -L | Integer | 20 | Length of region used to judge hits |
| -Y | Real | 0 | Effective length of the search space (use zero for the real size) |